PLMD::multicolvar::VolumeCavity Member List

This is the complete list of members for PLMD::multicolvar::VolumeCavity, including all inherited members.

ablocksPLMD::multicolvar::MultiColvarBaseprotected
Action(const ActionOptions &)PLMD::Actionexplicit
ActionAtomistic(const ActionOptions &ao)PLMD::ActionAtomisticexplicit
ActionVolume(const ActionOptions &)PLMD::multicolvar::ActionVolumeexplicit
ActionWithValue(const ActionOptions &ao)PLMD::ActionWithValueexplicit
ActionWithVessel(const ActionOptions &ao)PLMD::vesselbase::ActionWithVesselexplicit
activate()PLMD::Actionvirtual
activateTheseTasks(std::vector< unsigned > &addtionalTasks)PLMD::vesselbase::ActionWithVessel
addBridgeForces(const std::vector< double > &bb)PLMD::multicolvar::VolumeGradientBase
addBridgingVessel(ActionWithVessel *tome)PLMD::vesselbase::ActionWithVesselprotected
addComponent(const std::string &name)PLMD::ActionWithValue
addComponentWithDerivatives(const std::string &name)PLMD::ActionWithValue
addDependency(Action *)PLMD::Action
addTaskToList(const unsigned &taskCode)PLMD::multicolvar::MultiColvarBaseprotected
addValue()PLMD::ActionWithValue
addValueWithDerivatives()PLMD::ActionWithValue
addVessel(const std::string &name, const std::string &input, const int numlab=0)PLMD::vesselbase::ActionWithVesselprotected
addVessel(Vessel *vv)PLMD::vesselbase::ActionWithVesselprotected
allowToAccessGlobalForces()PLMD::ActionAtomisticinline
apply()PLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
applyBridgeForces(const std::vector< double > &bb)PLMD::multicolvar::BridgedMultiColvarFunctionvirtual
applyForces()PLMD::ActionAtomistic
applyPbc(std::vector< Vector > &dlist, unsigned max_index=0) const PLMD::multicolvar::MultiColvarBase
atomsPLMD::ActionAtomisticprotected
biPLMD::multicolvar::VolumeCavityprivate
boxfilePLMD::multicolvar::VolumeCavityprivate
boxoutPLMD::multicolvar::VolumeCavityprivate
BridgedMultiColvarFunction(const ActionOptions &)PLMD::multicolvar::BridgedMultiColvarFunctionexplicit
bridgeVariablePLMD::vesselbase::ActionWithVesselprotected
buildDataStashes(const bool &allow_wcutoff, const double &wtol)PLMD::vesselbase::ActionWithVessel
calculate()PLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
calculateAllVessels(const unsigned &taskCode, MultiValue &myvals, MultiValue &bvals, std::vector< double > &buffer, std::vector< unsigned > &der_list)PLMD::vesselbase::ActionWithVesselprotected
calculateAllVolumes(const unsigned &curr, MultiValue &outvals) const PLMD::multicolvar::ActionVolumevirtual
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum)PLMD::ActionAtomistic
calculateCentralAtomPosition()PLMD::multicolvar::BridgedMultiColvarFunctioninline
calculateFromPDB(const PDB &)PLMD::Action
calculateNumberInside(const Vector &cpos, Vector &derivatives, Tensor &vir, std::vector< Vector > &refders) const PLMD::multicolvar::VolumeCavityvirtual
calculateNumericalDerivatives(ActionWithValue *a=NULL)PLMD::multicolvar::BridgedMultiColvarFunctionvirtual
calculateWeight(AtomValuePack &myatoms) const PLMD::multicolvar::MultiColvarBasevirtual
changeBox(const Tensor &newbox)PLMD::ActionAtomistic
checkFieldsAllowed()PLMD::ActionWithValueinlinevirtual
checkNeedsGradients() const PLMD::Actioninlinevirtual
PLMD::checkNumericalDerivatives() const PLMD::Actioninlinevirtual
PLMD::ActionWithValue::checkNumericalDerivatives() const PLMD::ActionWithValueinlinevirtual
checkRead()PLMD::Action
checkUpdate() const PLMD::Action
cite(const std::string &s)PLMD::Action
clearDependencies()PLMD::Action
clearDerivatives()PLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
clearInputForces()PLMD::ActionWithValue
clearOptions()PLMD::Actionvirtual
clearOutputForces()PLMD::ActionAtomistic
commPLMD::Action
completeTask(const unsigned &curr, MultiValue &invals, MultiValue &outvals) const PLMD::multicolvar::VolumeGradientBasevirtual
componentIsNotPeriodic(const std::string &name)PLMD::ActionWithValue
componentIsPeriodic(const std::string &name, const std::string &min, const std::string &max)PLMD::ActionWithValue
componentsAreNotOptional(Keywords &keys)PLMD::ActionWithValuestatic
compute(const unsigned &tindex, AtomValuePack &myvals) const PLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
contributorsAreUnlockedPLMD::vesselbase::ActionWithVesselprotected
copyOutput(const std::string &name) const PLMD::ActionWithValue
copyOutput(const unsigned &n) const PLMD::ActionWithValue
crossPLMD::multicolvar::VolumeCavityprivate
dbiPLMD::multicolvar::VolumeCavityprivate
dcrossPLMD::multicolvar::VolumeCavityprivate
deactivate()PLMD::Actioninlinevirtual
deactivate_task(const unsigned &taskno)PLMD::multicolvar::BridgedMultiColvarFunctionvirtual
deactivateAllAtoms()PLMD::multicolvar::BridgedMultiColvarFunctionprotected
deactivateAllTasks()PLMD::vesselbase::ActionWithVesselprotected
deactivateTasksInRange(const unsigned &lower, const unsigned &upper)PLMD::vesselbase::ActionWithVesselprotected
decodeIndexToAtoms(const unsigned &taskCode, std::vector< unsigned > &atoms) const PLMD::multicolvar::MultiColvarBaseprotected
decoderPLMD::multicolvar::MultiColvarBaseprotected
Dependencies typedefPLMD::Action
derivativesAreRequired() const PLMD::vesselbase::ActionWithVesselinline
dlbiPLMD::multicolvar::VolumeCavityprivate
dlcrossPLMD::multicolvar::VolumeCavityprivate
dlperpPLMD::multicolvar::VolumeCavityprivate
doCalculation(const unsigned &tindex, AtomValuePack &myatoms) const PLMD::multicolvar::MultiColvarBasevirtual
doJobsRequiredBeforeTaskList()PLMD::multicolvar::VolumeGradientBasevirtual
doNotCalculateDerivatives() const PLMD::ActionWithValueinline
doNotCalculateDirector()PLMD::multicolvar::MultiColvarBaseinlinevirtual
doNotForce()PLMD::ActionAtomisticinline
doNotRetrieve()PLMD::ActionAtomisticinline
dperpPLMD::multicolvar::VolumeCavityprivate
error(const std::string &msg) const PLMD::Action
exists(const std::string &name) const PLMD::ActionWithValue
exit(int c=0)PLMD::Action
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
filesPLMD::Action
files_iterator typedefPLMD::Action
finishComputations(const std::vector< double > &buffer)PLMD::vesselbase::ActionWithVesselvirtual
finishTaskListUpdate()PLMD::vesselbase::ActionWithVesselinlinevirtual
fopen(const char *path, const char *mode)PLMD::Action
getAbsoluteIndex(int i) const PLMD::ActionAtomisticinline
getAbsoluteIndexes() const PLMD::ActionAtomisticinline
getActiveTask(const unsigned &ii) const PLMD::vesselbase::ActionWithVesselinlineprotected
getBox() const PLMD::multicolvar::VolumeGradientBaseinlineprotected
getCentralAtomElementIndex()PLMD::multicolvar::ActionVolumeinline
getCentralAtomPack(const unsigned &basn, const unsigned &curr)PLMD::multicolvar::BridgedMultiColvarFunctionvirtual
getCentralAtomPos(const unsigned &curr)PLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
getCharge(int i) const PLMD::ActionAtomisticinline
getComponentsList() const PLMD::ActionWithValue
getComponentsVector() const PLMD::ActionWithValue
getCurrentNumberOfActiveTasks() const PLMD::vesselbase::ActionWithVesselinlineprotected
getDependencies() const PLMD::Actioninline
getDocumentation() const PLMD::Actionvirtual
getEnergy() const PLMD::ActionAtomisticinline
getExchangeStep() const PLMD::Action
getForcesFromVessels(std::vector< double > &forcesToApply)PLMD::vesselbase::ActionWithVesselprotected
getFullNumberOfTasks() const PLMD::vesselbase::ActionWithVesselinline
getIndexList(const unsigned &ntotal, const unsigned &jstore, const unsigned &maxder, std::vector< unsigned > &indices)PLMD::multicolvar::BridgedMultiColvarFunction
getKernelType() const PLMD::multicolvar::ActionVolumeinlineprotected
getLabel() const PLMD::Actioninline
getMass(int i) const PLMD::ActionAtomisticinline
getName() const PLMD::Actioninline
getNLTolerance() const PLMD::vesselbase::ActionWithVesselinlineprotected
getNumberOfAtoms() const PLMD::ActionAtomisticinline
getNumberOfComponents() const PLMD::ActionWithValueinline
getNumberOfDerivatives()PLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
getNumberOfQuantities()PLMD::multicolvar::ActionVolumeinlinevirtual
getNumberOfVessels() const PLMD::vesselbase::ActionWithVesselinlineprotected
getOutputQuantity(const unsigned j) const PLMD::ActionWithValueinline
getOutputQuantity(const std::string &name) const PLMD::ActionWithValueinline
getPbc() const PLMD::multicolvar::VolumeGradientBaseinlineprotected
getPntrToComponent(int i)PLMD::ActionWithValueprotected
getPntrToComponent(const std::string &name)PLMD::ActionWithValueprotected
getPntrToMultiColvar() const PLMD::multicolvar::BridgedMultiColvarFunctioninline
getPntrToValue()PLMD::ActionWithValueprotected
getPntrToVessel(const unsigned &i)PLMD::vesselbase::ActionWithVesselinlineprotected
getPosition(int iatom) const PLMD::multicolvar::VolumeGradientBaseinlineprotected
PLMD::multicolvar::BridgedMultiColvarFunction::getPosition(AtomNumber) const PLMD::ActionAtomisticinline
getPositionInFullTaskList(const unsigned &ii) const PLMD::vesselbase::ActionWithVesselinline
getPositionOfAtomForLinkCells(const unsigned &iatom) const PLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
getPositions() const PLMD::ActionAtomisticinline
getRestart() const PLMD::Actioninline
getSeparation(const Vector &vec1, const Vector &vec2) const PLMD::multicolvar::MultiColvarBaseprotected
getSigma() const PLMD::multicolvar::ActionVolumeinlineprotected
getSizeOfAtomsWithDerivatives()PLMD::multicolvar::BridgedMultiColvarFunctioninline
getSizeOfBuffer(unsigned &bufsize)PLMD::vesselbase::ActionWithVesselprotected
getStep() const PLMD::Action
getTaskCode(const unsigned &ii) const PLMD::vesselbase::ActionWithVesselinline
getTime() const PLMD::Action
getTimeStep() const PLMD::Action
getTolerance() const PLMD::vesselbase::ActionWithVesselinlineprotected
getTotAtoms() const PLMD::ActionAtomisticinline
getUnique() const PLMD::ActionAtomisticinline
getVesselWithName(const std::string &mynam)PLMD::vesselbase::ActionWithVessel
hasDifferentiableOrientation() const PLMD::multicolvar::MultiColvarBaseinlinevirtual
inVolumeOfInterest(const unsigned &curr) const PLMD::multicolvar::ActionVolume
isActive() const PLMD::Actioninline
isCurrentlyActive(const unsigned &, const unsigned &)PLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
isDensity() const PLMD::multicolvar::MultiColvarBaseinlinevirtual
isOptionOn(const std::string &s) const PLMD::Actioninline
isPeriodic()PLMD::multicolvar::BridgedMultiColvarFunctionvirtual
jacob_detPLMD::multicolvar::VolumeCavityprivate
keywordsPLMD::Action
len_biPLMD::multicolvar::VolumeCavityprivate
len_crossPLMD::multicolvar::VolumeCavityprivate
len_perpPLMD::multicolvar::VolumeCavityprivate
lenunitPLMD::multicolvar::VolumeCavityprivate
lockContributors()PLMD::vesselbase::ActionWithVessel
lockRequests()PLMD::ActionAtomisticinlinevirtual
logPLMD::Action
makeWhole()PLMD::ActionAtomistic
modifyForceOnEnergy()PLMD::ActionAtomisticinline
modifyForces()PLMD::ActionAtomisticinline
modifyGlobalForce(AtomNumber)PLMD::ActionAtomisticinline
modifyGlobalVirial()PLMD::ActionAtomisticinline
modifyPosition(AtomNumber)PLMD::ActionAtomisticinline
modifyVirial()PLMD::ActionAtomisticinline
multi_sim_commPLMD::Action
PLMD::multicolvar::MultiColvarBase::MultiColvarBase(const ActionOptions &)PLMD::multicolvar::MultiColvarBaseexplicit
nblockPLMD::multicolvar::MultiColvarBaseprotected
needsDerivatives()PLMD::vesselbase::ActionWithVesselprotected
noAnalyticalDerivatives(Keywords &keys)PLMD::ActionWithValuestatic
originPLMD::multicolvar::VolumeCavityprivate
parse(const std::string &key, T &t)PLMD::Action
parseAtomList(const std::string &key, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
parseAtomList(const std::string &key, const int num, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
parseFlag(const std::string &key, bool &t)PLMD::Action
parseNumbered(const std::string &key, const int no, T &t)PLMD::Action
parseNumberedVector(const std::string &key, const int no, std::vector< T > &t)PLMD::Action
parseVector(const std::string &key, std::vector< T > &t)PLMD::Action
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) const PLMD::ActionAtomistic
pbcDistance(const Vector &v1, const Vector &v2) const PLMD::multicolvar::VolumeGradientBaseinlineprotected
performTask(const unsigned &, const unsigned &, MultiValue &) const PLMD::multicolvar::BridgedMultiColvarFunctionvirtual
perpPLMD::multicolvar::VolumeCavityprivate
plumedPLMD::Action
prepare()PLMD::Actionvirtual
readAtomsFromPDB(const PDB &pdb)PLMD::ActionAtomisticvirtual
readVesselKeywords()PLMD::vesselbase::ActionWithVesselprotected
registerKeywords(Keywords &keys)PLMD::multicolvar::VolumeCavitystatic
requestAtoms(const std::vector< AtomNumber > &atoms)PLMD::multicolvar::VolumeGradientBaseprotected
resizeFunctions()PLMD::vesselbase::ActionWithVesselprotected
retrieveAtoms()PLMD::ActionAtomistic
retrieveCentralAtomPos()PLMD::multicolvar::BridgedMultiColvarFunction
retrieveDomain(std::string &min, std::string &max)PLMD::vesselbase::ActionWithVesselvirtual
runAllTasks()PLMD::vesselbase::ActionWithVesselprotected
runFinalJobs()PLMD::Actioninlinevirtual
serialCalculation() const PLMD::vesselbase::ActionWithVesselinlineprotected
setAtomActive(const unsigned &n)PLMD::multicolvar::BridgedMultiColvarFunctionprotected
setAtomsForCentralAtom(const std::vector< bool > &catom_ind)PLMD::multicolvar::MultiColvarBaseprotected
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0)PLMD::ActionAtomistic
setGradientsIfNeeded()PLMD::ActionWithValue
setLinkCellCutoff(const double &lcut)PLMD::multicolvar::MultiColvarBaseprotected
setLowMemOption(const bool &)PLMD::vesselbase::ActionWithVesselinlineprotected
setNotPeriodic()PLMD::ActionWithValue
setNumberInVolume(const unsigned &, const unsigned &, const double &, const Vector &, const Tensor &, const std::vector< Vector > &, MultiValue &) const PLMD::multicolvar::VolumeGradientBaseprotected
setOption(const std::string &s)PLMD::Actionvirtual
setPeriodic(const std::string &min, const std::string &max)PLMD::ActionWithValue
setupCurrentAtomList(const unsigned &taskCode, AtomValuePack &myatoms) const PLMD::multicolvar::MultiColvarBaseprotected
setupLinkCells()PLMD::multicolvar::MultiColvarBaseprotected
setupMultiColvarBase()PLMD::multicolvar::MultiColvarBaseprotected
setupRegions()PLMD::multicolvar::VolumeCavityvirtual
setValue(const double &d)PLMD::ActionWithValueinlineprotected
setValue(Value *, double)PLMD::ActionWithValue
sigmaPLMD::multicolvar::VolumeCavityprivate
storedValueIsActive(const unsigned &iatom)PLMD::multicolvar::MultiColvarBase
transformBridgedDerivatives(const unsigned &current, MultiValue &invals, MultiValue &outvals) const PLMD::multicolvar::BridgedMultiColvarFunctionvirtual
turnOnDerivatives()PLMD::multicolvar::MultiColvarBasevirtual
unlockContributors()PLMD::vesselbase::ActionWithVessel
unlockRequests()PLMD::ActionAtomisticinlinevirtual
update()PLMD::multicolvar::VolumeCavityvirtual
updateActiveAtoms(AtomValuePack &myatoms) const PLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
useCustomisableComponents(Keywords &keys)PLMD::ActionWithValuestatic
useNumericalDerivatives()PLMD::ActionWithValueinline
usesPbc() const PLMD::multicolvar::MultiColvarBaseinline
usespeciesPLMD::multicolvar::MultiColvarBaseprotected
usingLowMem() const PLMD::vesselbase::ActionWithVesselinlineprotected
VolumeCavity(const ActionOptions &ao)PLMD::multicolvar::VolumeCavityexplicit
VolumeGradientBase(const ActionOptions &)PLMD::multicolvar::VolumeGradientBaseexplicit
warning(const std::string &msg)PLMD::Action
weightHasDerivativesPLMD::vesselbase::ActionWithVesselprotected
weightWithDerivatives() const PLMD::vesselbase::ActionWithVesselinline
~Action()PLMD::Actionvirtual
~ActionAtomistic()PLMD::ActionAtomistic
~ActionWithValue()PLMD::ActionWithValue
~ActionWithVessel()PLMD::vesselbase::ActionWithVessel
~MultiColvarBase()PLMD::multicolvar::MultiColvarBaseinline
~VolumeCavity()PLMD::multicolvar::VolumeCavity
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